Rapid Catalytic Template Searching as an Enzyme Function Prediction Procedure

SABER: A computational method for identifying active sites for new reactions

(2012) Geoffrey R. Nosrati et al.   PROTEIN SCIENCE

Divergent Evolution in Enolase Superfamily: Strategies for Assigning Functions

(2011) John A. Gerlt et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Active site prediction using evolutionary and structural information

(2010) Sriram Sankararaman et al.   BIOINFORMATICS

The LabelHash algorithm for substructure matching

(2010) Mark Moll et al.   BMC BIOINFORMATICS

SMAP-WS: a parallel web service for structural proteome-wide ligand-binding site comparison

(2010) J. Ren et al.   NUCLEIC ACIDS RESEARCH

Derivation of 3D coordinate templates for searching structural databases: Application to ser-His-Asp catalytic triads in the serine proteinases and lipases

(2010) Andrew C. Wallace et al.   PROTEIN SCIENCE

A unified statistical model to support local sequence order independent similarity searching for ligand-binding sites and its application to genome-based drug discovery

(2009) L. Xie et al.   BIOINFORMATICS

EFICAz2: enzyme function inference by a combined approach enhanced by machine learning

(2009) Adrian K Arakaki et al.   BMC BIOINFORMATICS

FINDSITE: a combined evolution/structure-based approach to protein function prediction

(2009) J. Skolnick et al.   BRIEFINGS IN BIOINFORMATICS

Identifying and Characterizing Binding Sites and Assessing Druggability

(2009) Thomas A. Halgren   Journal of Chemical Information and Modeling

Predicting Protein Function and Binding Profile via Matching of Local Evolutionary and Geometric Surface Patterns

(2009) Yan Yuan Tseng et al.   JOURNAL OF MOLECULAR BIOLOGY

Tess: A geometric hashing algorithm for deriving 3D coordinate templates for searching structural databases. Application to enzyme active sites

(2009) Andrew C. Wallace et al.   PROTEIN SCIENCE

INTREPID—INformation-theoretic TREe traversal for Protein functional site IDentification

(2008) Sriram Sankararaman et al.   BIOINFORMATICS

Kemp elimination catalysts by computational enzyme design

(2008) Daniela Röthlisberger et al.   NATURE

BLOSUM62 miscalculations improve search performance

(2008) Mark P Styczynski et al.   NATURE BIOTECHNOLOGY

Detecting evolutionary relationships across existing fold space, using sequence order-independent profile-profile alignments

(2008) L. Xie et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Discovery of a Dipeptide Epimerase Enzymatic Function Guided by Homology Modeling and Virtual Screening

(2008) Chakrapani Kalyanaraman et al.   STRUCTURE